3run: Difference between revisions

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 ==New strategy to analyze structures of glycopeptide antibiotic-target complexes==
-<StructureSection load='3run' size='340' side='right' caption='[[3run]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
+<StructureSection load='3run' size='340' side='right'caption='[[3run]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3run]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Amycolatopsis_orientalis Amycolatopsis orientalis] and [http://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RUN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RUN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3run]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpt4 Bpt4] and [https://en.wikipedia.org/wiki/Streptomyces_orientalis Streptomyces orientalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RUN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RUN FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=RER:(1R,3S,4S,5S)-3-AMINO-2,3,6-TRIDEOXY-3-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSE'>RER</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=RER:(1R,3S,4S,5S)-3-AMINO-2,3,6-TRIDEOXY-3-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSE'>RER</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3FG:(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC+ACID'>3FG</scene>, <scene name='pdbligand=CCS:CARBOXYMETHYLATED+CYSTEINE'>CCS</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=GHP:(2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC+ACID'>GHP</scene>, <scene name='pdbligand=MLU:N-METHYL-D-LEUCINE'>MLU</scene>, <scene name='pdbligand=OMY:(BETAR)-3-CHLORO-BETA-HYDROXY-L-TYROSINE'>OMY</scene>, <scene name='pdbligand=OMZ:(BETAR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE'>OMZ</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2lzm|2lzm]], [[3rul|3rul]], [[3rum|3rum]], [[3vfj|3vfj]], [[3vfk|3vfk]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2lzm|2lzm]], [[3rul|3rul]], [[3rum|3rum]], [[3vfj|3vfj]], [[3vfk|3vfk]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">E ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3run FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3run OCA], [http://pdbe.org/3run PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3run RCSB], [http://www.ebi.ac.uk/pdbsum/3run PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3run ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3run FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3run OCA], [https://pdbe.org/3run PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3run RCSB], [https://www.ebi.ac.uk/pdbsum/3run PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3run ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/LYS_BPT4 LYS_BPT4]] Helps to release the mature phage particles from the cell wall by breaking down the peptidoglycan.
+[[https://www.uniprot.org/uniprot/LYS_BPT4 LYS_BPT4]] Helps to release the mature phage particles from the cell wall by breaking down the peptidoglycan.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 29: / Line 29: @@
 __TOC__
 </StructureSection>
-[[Category: Amycolatopsis orientalis]]
 [[Category: Bpt4]]
+[[Category: Large Structures]]
 [[Category: Lysozyme]]
+[[Category: Streptomyces orientalis]]
 [[Category: Economou, N J]]
 [[Category: Loll, P J]]